Background proteome not digesting gmurray  2019-11-13

Hi there,

Recently installed Skyline on Win10. Trying to create a background proteome with no luck. I can successfully create the .protdb file containing 10,000 proteins from a single FASTA file; however, when I select my enzyme it fails to digest this background.

Any help would be appreciated.

Many thanks,


Nick Shulman responded:  2019-11-13
It used to be that the .protdb needed to be indexed in different ways depending on which enzyme you have selected.

About two years ago we changed the way that the file gets indexed that works for all enzymes. It is no longer necessary for the background proteome to be digested.

It sounds like Skyline is giving you some sort of spurious message about the file needing to be digested. Can you post a screenshot of what you are seeing? It might be that Skyline has gotten stuck somewhere and you are seeing a message was supposed to disappear after a fraction of a second, or there might be some bug in our logic somewhere.

-- Nick